Yes. No? The checksum does not include the header: IIRC, the computation begins at address 0x200 and continues from there to the end of the file.
Ah, okay. That sounds a lot more manageable. I wonder what the calculation would be if it did include the header, theoretically.
The checksum word would be included as part of the sum too as it's stored in the header, there's only one possible solution in this situation, and that's if all other words sum up to 0000, then the checksum word itself can be anything and always correct. So you either; hope for 0000 result, skip the checksum word during the sum, or store a second counter word which holds the negative polar opposite of the checksum word itself, so they cancel each other out.
It should be noted that the Wing Fortress Zone and Super Sonic bugfixes were inherited in Sonic 3. It's easier to see the Super Sonic fix in the November 3 prototype, since Sonic doesn't quite have his double-jump moves yet.